The Code Breaker Page 5

  In early 2000, as the competition became a public spectacle, President Bill Clinton pushed for a truce between Venter and Collins, who had been sniping at each other in the press. Collins had likened Venter’s sequencing to “Cliff’s Notes” and “Mad magazine”; Venter had ridiculed the government project for costing ten times more to do work at a fraction of the speed. “Fix it—make these guys work together,” Clinton told his top science advisor. So Collins and Venter met for pizza and beer to see if they could reach an accord on sharing the credit and agreeing to make public, rather than exploiting for private use, what would soon be the world’s most important biological data set.

  After a few more private meetings, Clinton was able to host Collins and Venter at a White House ceremony to announce the initial results of the Human Genome Project and the agreement to share credit. James Watson hailed the decision. “The events of the past few weeks have shown that those who work for the public good do not necessarily fall behind those driven by personal gain,” he said.

  I was editor of Time then, and we had been working with Venter for weeks to have exclusive access to his story and feature him on the cover. He was an enticing cover boy, because by then he had used his wealth from Celera to become a flashy yacht-owner, competitive surfer, and party-giver. The week that we were closing the story, I got an unexpected phone call from Vice President Al Gore. He pushed me—very hard and persuasively—to put Francis Collins on the cover as well. Venter resisted. He had been forced to share credit with Collins at a press conference, but he did not want to also share a Time cover. He eventually agreed, but at the photo session he could not help ragging on Collins for not being able to keep pace with Celera’s sequencing. Collins smiled and said nothing.6

  “Today we are learning the language in which God created life,” President Clinton proclaimed at the White House ceremony featuring Venter, Collins, and Watson. The announcement captured the public imagination. The New York Times ran a front-page banner headline, “Genetic Code of Human Life Is Cracked by Scientists.” The story, written by the distinguished biology journalist Nicholas Wade, began, “In an achievement that represents a pinnacle of human self-knowledge, two rival groups of scientists said today that they had deciphered the hereditary script, the set of instructions that defines the human organism.”7

  * * *

  Doudna spent time discussing with Szostak, Church, and others at Harvard whether the $3 billion dedicated to the Human Genome Project was worth it. Church was skeptical at the time, and remains so. “The three billion dollars didn’t buy us much,” he says. “We didn’t discover anything. None of the technologies survived.” Having a map of DNA did not, it turned out, lead to most of the grand medical breakthroughs that had been predicted. More than four thousand disease-causing DNA mutations were found. But no cure sprang forth for even the most simple of single-gene disorders, such as Tay-Sachs, sickle cell, or Huntington’s. The men who had sequenced DNA taught us how to read the code of life, but the more important step would be learning how to write that code. This would require a different set of tools, ones that would involve the worker-bee molecule that Doudna found more interesting than DNA.

  Jack Szostak

  CHAPTER 6 RNA

  The central dogma

  Accomplishing the goal of being able to write as well as to read human genes required a shift in focus from DNA to its less famous sibling that actually carries out its coded instructions. RNA (ribonucleic acid) is a molecule in living cells that is similar to DNA (deoxyribonucleic acid), but it has one more oxygen atom in its sugar-phosphate backbone and a difference in one of its four bases.

  DNA may be the world’s most famous molecule, so well-known that it appears on magazine covers and is used as a metaphor for traits that are ingrained in a society or organization. But like many famous siblings, DNA doesn’t do much work. It mainly stays at home in the nucleus of our cells, not venturing forth. Its primary activity is protecting the information it encodes and occasionally replicating itself. RNA, on the other hand, actually goes out and does real work. Instead of just sitting at home curating information, it makes real products, such as proteins. Pay attention to it. From CRISPR to COVID, it will be the starring molecule in this book and in Doudna’s career.

  At the time of the Human Genome Project, RNA was seen as mainly a messenger molecule that carries instructions from the DNA that is nestled in the nucleus of the cells. A small segment of DNA that encodes a gene is transcribed into a snippet of RNA, which then travels to the manufacturing region of the cell. There this “messenger RNA” facilitates the assembly of the proper sequence of amino acids to make a specified protein.

  These proteins come in many types. Fibrous proteins, for example, form structures such as bones, tissues, muscles, hair, fingernails, tendons, and skin cells. Membrane proteins relay signals within cells. Above all is the most fascinating type of proteins: enzymes. They serve as catalysts. They spark and accelerate and modulate the chemical reactions in all living things. Almost every action that takes place in a cell needs to be catalyzed by an enzyme. Pay attention to enzymes. They will be RNA’s costars and dancing partners in this book.

  Francis Crick, five years after co-discovering the structure of DNA, came up with a name for this process of genetic information moving from DNA to RNA to the building of proteins. He dubbed it the “central dogma” of biology. He later conceded that “dogma,” which implies an unchanging and unquestioned faith, was a poor choice of words.1 But the word “central” was apt. Even as the dogma was modified, the process remained central to biology.

  Ribozymes

  One of the first tweaks to the central dogma came when Thomas Cech and Sidney Altman independently discovered that proteins were not the only molecules in the cell that could be enzymes. In work done in the early 1980s that would win them the Nobel Prize, they made the surprising discovery that some forms of RNA could likewise be enzymes. Specifically, they found that some RNA molecules can split themselves by sparking a chemical reaction. They dubbed these catalytic RNAs “ribozymes,” a word conjured up by combining “ribonucleic acid” with “enzyme.”2

  Cech and Altman made this discovery by studying introns. Some parts of DNA sequences do not code instructions for how to make proteins. When these sequences are transcribed into RNA molecules, they clog things up. So they have to be sliced out before the RNA can scurry out on its mission to direct the making of proteins. The cut-and-paste process of slicing out these introns and then splicing the useful bits of RNA back together requires a catalyst, and that role is usually performed by a protein enzyme. But Cech and Altman discovered that there were certain RNA introns that were self-splicing!

  This had pretty cool implications. If some RNA molecules could store genetic information and also act as a catalyst to spur chemical reactions, they might be more fundamental to the origins of life than DNA, which cannot naturally replicate themselves without the presence of proteins to serve as a catalyst.3

  RNA rather than DNA

  When Doudna’s lab rotation ended in the spring of 1986, she asked Jack Szostak if she could stay on and do her doctoral research under him. Szostak agreed—but he added a caveat. He was no longer going to focus on DNA in yeast. While other biochemists were getting excited about sequencing DNA for the Human Genome Project, he had decided to shift his lab’s attention to RNA, which he believed might reveal secrets about the biggest of all biological mysteries: the origins of life.

  He was intrigued, he told Doudna, by the discoveries that Cech and Altman had made about how certain RNAs had the catalytic powers of enzymes. His goal was to pin down whether these ribozymes could use this power to replicate. “Did this piece of RNA have the chemical chops to copy itself?” he asked her. He suggested that should be the focus of her PhD dissertation.4

  She found Szostak’s enthusiasm infectious and signed up to be the first graduate student in his lab to work on RNA. “When I was taught biology, we learned about the structure and code of DNA, and we learned about how proteins do all the heavy lifting in cells, and RNA was treated as this dull intermediary, sort of a middle manager,” she recalls. “I was quite surprised to find that there was this young genius, Jack Szostak, at Harvard who wanted to focus a hundred percent on RNA because he thought that it was the key to understanding the origin of life.”

  For both Szostak, who was well established, and Doudna, who wasn’t, switching to a focus on RNA was risky. “Instead of following the herd doing DNA,” Szostak recalled, “we felt we were pioneering something new, exploring a frontier that was a little bit neglected but we all thought was exciting.” This was long before RNA was being considered as a technology to interfere with gene expression or deliver edits to human genes. Szostak and Doudna pursued the subject out of pure curiosity about how nature works.

  Szostak had a guiding principle: Never do something that a thousand other people are doing. That appealed to Doudna. “It was like when I was on the soccer field and wanted to play a position that the other kids didn’t,” she says. “I learned from Jack that there was more of a risk but also more of a reward if you ventured into a new area.”

  By this point she knew that the most important clue for understanding a natural phenomenon was to figure out the structure of the molecules involved. That would require her to learn some of the techniques that Watson and Crick and Franklin used to unravel the structure of DNA. If she and Szostak succeeded, it could be a significant step in answering one of the grandest of all biological questions, perhaps the grandest: How did life begin?

  The origins of life

  Szostak’s excitement about discovering how life began taught Doudna a second big lesson, in addition to taking risks by moving into new fields: Ask big questions. Even though Szostak liked diving into the details of experiments, he was a grand thinker, someone who was constantly pursuing truly profound inquiries. “Why else would you do science?” he asked Doudna. It was an injunction that became one of her own guiding principles.5

  There are some truly grand questions that our mortal minds may never be able to answer: How did the universe begin? Why is there something rather than nothing? What is consciousness? Others may be wrestled into submission by the end of this century: Is the universe deterministic? Do we have free will? Of the really big ones, the closest to being solved is how life began.

  The central dogma of biology requires the presence of DNA, RNA, and proteins. Because it’s unlikely that all three of these sprang forth at the exact same time from the primordial stew, a hypothesis arose in the early 1960s—formulated independently by the ubiquitous Francis Crick and others—that there was a simpler precursor system. Crick’s hypothesis was that, early on in the history of earth, RNA was able to replicate itself. That leaves the question of where the first RNA came from. Some speculate it came from outer space. But the simpler answer may be that the early earth contained the chemical building blocks of RNA, and it didn’t require anything other than natural random mixing to jostle them together. The year that Doudna joined Szostak’s lab, biochemist Walter Gilbert dubbed this hypothesis “the RNA world.”6

  * * *

  An essential quality of living things is that they have a method for creating more organisms akin to themselves: they can reproduce. Therefore, if you want to make the argument that RNA might be the precursor molecule leading to the origin of life, it would help to show how it can replicate itself. This was the project that Szostak and Doudna embarked upon.7

  Doudna used many tactics to create an RNA enzyme, or ribozyme, that could stitch together little RNA pieces. Eventually, she and Szostak were able to engineer a ribozyme that could splice together a copy of itself. “This reaction demonstrates the feasibility of RNA-catalyzed RNA replications,” she and Szostak wrote in a 1998 paper for Nature. The biochemist Richard Lifton later called this paper a “technical tour de force.”8 Doudna became a rising star in the rarefied realm of RNA research. That was still a bit of a biological backwater, but over the next two decades the understanding of how little strands of RNA behaved would become increasingly important, both to the field of gene editing and to the fight against coronaviruses.

  * * *

  As a young PhD student, Doudna mastered the special combination of skills that distinguished Szostak and other great scientists: she was good at doing hands-on experiments and also at asking the big questions. She knew that God was in the details but also in the big picture. “Jennifer was fantastically good at the bench, because she was fast and sharp and could seemingly get anything to work,” Szostak says. “But we talked quite a bit about why the really big questions are the important questions.”

  Doudna also proved herself a team player, which counted a lot for Szostak, who shared that trait with George Church and some other scientists at the Harvard Medical School campus. This was reflected in the number of coauthors she had on most of her papers. In scientific publications, the first author listed is usually the younger researcher most responsible for the hands-on experiments, and the last is the principal investigator or head of the lab. Those listed in the middle are generally ordered by the contributions they made. On one of the important papers that she helped produce for the journal Science in 1989, Doudna’s name appears in the middle of the list because she was mentoring a lucky Harvard undergraduate who worked in the lab part time, and she felt that the student should be the featured lead author. During her final year in Szostak’s lab, her name was on four academic papers in prestigious journals, all describing aspects of how RNA molecules can replicate themselves.9

  What also stood out for Szostak was Doudna’s willingness, even eagerness, to tackle challenges. That became evident near the end of her tenure in Szostak’s lab in 1989. She realized that in order to understand the workings of a self-splicing piece of RNA, she would have to fully discern its structure, atom by atom. “At that time, RNA structure was viewed as so difficult that it was maybe impossible to figure out,” Szostak recalled. “Hardly anyone was trying anymore.”10

  Meeting James Watson

  The first time that Jennifer Doudna made a presentation at a scientific conference, it was at the Cold Spring Harbor Laboratory, and James Watson was, as usual, sitting in the front row as the host. It was the summer of 1987, and he had organized a seminar to discuss “the evolutionary events that may have given rise to the living organisms that now exist on earth.”11 In other words, how did life begin?

  The focus of the conference was on the recent discoveries showing that certain RNA molecules could replicate themselves. Because Szostak was unavailable, an invitation went out to Doudna, then only twenty-three, to present the work that she and he were doing on engineering a self-replicating RNA molecule. When she got the letter signed by Watson addressed to “Dear Ms. Doudna” (she was not yet Dr. Doudna), she not only immediately accepted; she had it framed.

  The talk she gave, based on a paper she had written with Szostak, was highly technical. “We describe deletions and substitution mutations in the catalytic and substrate domains of the self-splicing intron,” she began. That’s the type of sentence that excites research biologists, and Watson was intently taking notes. “I was so incredibly nervous that my palms were sweating,” she recalls. But at the end, Watson congratulated her, and Tom Cech, whose work on introns had paved the way for Doudna and Szostak’s paper, leaned over and whispered, “Good job.”12

  While at the meeting, Doudna took a walk down Bungtown Road, which wanders through the campus. Along the way, she saw a slightly stooped woman walking toward her. It was the biologist Barbara McClintock, who had been a researcher at Cold Spring Harbor for more than forty years and had recently been awarded the Nobel Prize for her discovery of transposons, known as “jumping genes,” that can change their position in a genome. Doudna paused, but was too shy to introduce herself. “I felt like I was in the presence of a goddess,” she says, still in awe. “Here’s this woman who’s so famous and so incredibly influential in science acting so unassuming and walking toward her lab thinking about her next experiment. She was what I wanted to be.”

  Doudna would stay in touch with Watson, attending many of the Cold Spring Harbor meetings he organized. Over the years, he would evolve into an increasingly controversial character because of his unmoored blurtings about racial genetic differences. Doudna generally refrained from letting his behavior diminish her respect for his scientific achievements. “When I saw him, he often would say things he thought were provocative,” she says with a slightly defensive laugh. “That was his way. You know how it is.” Despite his frequent public comments about women’s looks, beginning with Rosalind Franklin in The Double Helix, he was a good mentor to women. “He was very supportive to a close woman friend of mine who was a postdoc,” Doudna says. “That influenced my opinion of him.”

  CHAPTER 7 Twists and Folds

  Structural biology

  Ever since she puzzled over the touch-sensitive leaves of the sleeping grass that she found on her walks as a child in Hawaii, Doudna had been passionately curious about the underlying mechanisms of nature. What made the fernlike leaves curl when touched? How did chemical reactions cause biological activity? She learned how to pause, like we all used to do as children, and wonder about how things worked.